Contacts of the helix formed by residues 381 - 395 (chain B) in PDB entry 5OIV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 381 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B ILE 4.7 3.1 + - - +
362B SER* 4.1 2.9 + - - +
375B TYR* 2.9 40.3 + + - -
376B TRP* 3.4 61.1 - + + -
379B PRO 3.4 15.9 + - - -
380B VAL* 1.3 76.3 - - - +
382B PRO* 1.3 68.7 - - - +
383B VAL* 4.1 11.7 - - + -
384B LEU* 3.0 21.1 + - + +
385B THR* 3.1 14.0 + - - -
419B GLU* 3.4 44.0 - - + -
420B TYR* 3.4 28.4 - + + +
436B TRP* 3.9 22.4 - + - -
502B GOL 5.7 2.5 - - - -
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Residues in contact with PRO 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B VAL 3.6 10.1 - - - +
381B TRP* 1.3 82.4 - - - +
383B VAL* 1.3 56.7 + - - +
385B THR* 3.2 11.6 + - - +
386B TRP* 2.9 29.6 + - - +
408B GLY 6.2 0.2 - - - +
411B GLN* 3.8 11.0 - - - +
412B ALA* 6.1 3.4 - - + -
418B ALA 4.0 0.7 - - - +
419B GLU 3.6 16.2 - - - +
421B TYR* 3.8 29.6 - - + -
437B THR* 3.9 33.0 - - + +
440B ALA* 4.3 7.0 - - + +
441B VAL* 6.5 0.2 - - + -
444B TRP* 4.2 10.4 - - + -
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Residues in contact with VAL 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TRP* 5.3 5.6 - - + -
46B PHE* 3.5 41.0 - - + -
376B TRP* 4.6 7.4 - - + -
381B TRP* 4.1 17.3 - - + -
382B PRO* 1.3 78.1 - - - +
384B LEU* 1.3 62.8 + - + +
386B TRP* 3.3 6.9 + - - +
387B LEU* 3.0 27.3 + - - +
436B TRP* 3.6 60.7 - - + +
440B ALA* 5.4 0.7 - - - -
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TRP* 5.1 7.4 - - + -
181B MET* 4.2 11.0 - - + -
254B PHE* 3.9 31.6 - - + -
321B ALA* 4.0 27.4 - - + -
360B ILE* 5.2 10.3 - - + +
362B SER* 4.8 9.0 - - - -
376B TRP* 3.9 31.4 - - + -
381B TRP* 3.0 14.1 + - + +
383B VAL* 1.3 79.8 - - + +
385B THR* 1.3 66.0 + - - +
387B LEU* 3.8 8.5 - - + +
388B PHE* 2.8 42.0 + - + -
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Residues in contact with THR 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 3.7 24.2 - - + +
360B ILE* 5.1 7.4 + - - +
380B VAL* 4.3 10.2 - - - +
381B TRP 3.1 10.8 + - - -
382B PRO* 3.5 12.7 - - - +
384B LEU* 1.3 78.2 - - - +
386B TRP* 1.3 58.4 + - - +
388B PHE* 4.0 4.0 - - - +
389B SER* 2.9 30.3 + - - -
404B LEU* 3.5 35.5 - - + +
408B GLY* 4.3 2.7 - - - -
411B GLN* 5.2 0.5 + - - -
444B TRP* 3.6 18.4 - - + -
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Residues in contact with TRP 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 3.8 28.7 - + + -
49B ILE* 3.7 29.4 - - + -
121B ILE* 3.9 14.8 - - + -
125B ARG* 4.7 3.6 - - + -
382B PRO 2.9 14.1 + - - +
383B VAL* 3.6 8.1 - - - +
385B THR* 1.3 77.4 - - - +
387B LEU* 1.3 76.4 + - + +
389B SER* 3.0 4.4 + - - -
390B TRP* 2.9 58.2 + + + -
440B ALA* 3.8 27.1 - - + -
443B ASP* 2.7 40.9 + - + +
444B TRP* 3.3 35.9 - + + +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TRP* 4.9 3.8 - - + -
46B PHE* 4.7 10.5 - - + -
118B VAL* 4.6 12.3 - - + -
121B ILE* 4.1 21.1 - - + -
254B PHE* 4.2 20.6 - - + -
258B ILE* 4.0 30.3 - - + -
328B LEU* 4.6 5.4 - - + -
383B VAL 3.0 17.1 + - - +
384B LEU* 3.2 9.4 + - + +
386B TRP* 1.3 94.5 - - + +
388B PHE* 1.3 62.0 + - + +
390B TRP* 3.9 1.0 - - + +
391B CYS* 3.0 42.5 + - - -
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Residues in contact with PHE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B PHE* 3.8 26.7 - + - -
321B ALA* 3.7 25.6 - - + -
324B PHE* 3.7 24.7 - + + -
328B LEU* 3.7 25.8 - - + -
360B ILE* 3.6 24.5 - - + -
384B LEU* 2.8 51.3 + - + +
385B THR 4.0 1.3 - - - +
387B LEU* 1.3 72.6 - - + +
389B SER* 1.3 58.7 + - - +
391B CYS 3.4 0.3 + - - -
392B PHE* 2.8 56.3 + + + -
404B LEU* 3.9 17.0 - - + -
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Residues in contact with SER 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B THR 2.9 16.8 + - - -
386B TRP* 3.0 17.3 + - - -
388B PHE* 1.3 76.6 - - - +
390B TRP* 1.3 62.7 + - - +
392B PHE* 4.4 0.2 - - - -
393B ALA* 3.0 21.0 + - - +
401B ALA* 3.3 33.7 - - - +
404B LEU* 3.9 17.2 - - - +
405B ARG* 4.4 5.6 - - - -
444B TRP* 3.3 21.6 + - - -
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Residues in contact with TRP 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.8 43.1 - - + -
124B GLN* 3.9 28.9 - - + +
125B ARG* 3.8 19.8 - - - +
128B GLU* 5.1 0.8 + - - -
261B VAL* 4.0 9.9 - - + -
265B VAL* 3.8 17.0 - - + -
386B TRP* 2.9 49.0 + + + +
387B LEU* 3.9 1.6 - - + +
389B SER* 1.3 79.1 + - - +
391B CYS* 1.3 74.5 + - - +
393B ALA* 3.4 8.2 + - + +
394B ARG* 3.1 49.4 + - + +
443B ASP* 5.4 1.6 - - - -
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Residues in contact with CYS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 5.1 0.2 - - - -
261B VAL* 4.6 11.7 - - - -
328B LEU* 3.7 50.4 - - + +
387B LEU* 3.0 34.4 + - - +
388B PHE 4.0 0.4 - - - +
390B TRP* 1.3 98.0 - - - +
392B PHE* 1.3 65.1 + - + +
394B ARG* 3.2 8.2 + - - +
395B ARG* 3.0 25.9 + - - +
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Residues in contact with PHE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B LEU* 3.8 31.4 - - + -
328B LEU* 4.8 0.7 - - + -
341B LEU* 5.1 0.2 - - + -
344B LEU* 3.7 32.5 - - + -
360B ILE* 5.0 0.9 - - + -
388B PHE* 2.8 48.2 + + - +
389B SER 3.8 3.4 - - - +
391B CYS* 1.3 76.5 - - + +
393B ALA* 1.3 63.7 + - - +
395B ARG* 3.0 9.2 + - - +
397B TRP* 3.0 50.9 + + + +
400B ARG* 4.1 21.1 - - + -
401B ALA* 4.1 11.4 - - + +
404B LEU* 3.6 31.2 - - + -
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ALA 4.1 2.9 - - - +
396A GLY* 3.4 13.4 - - - +
398A ALA* 4.2 21.1 - - + +
389B SER 3.0 17.3 + - - +
390B TRP* 3.8 7.4 - - + +
391B CYS 3.3 0.2 - - - -
392B PHE* 1.3 76.1 - - - +
394B ARG* 1.3 56.4 + - - +
396B GLY* 3.0 17.8 + - - -
397B TRP 4.4 4.9 - - - +
398B ALA* 5.1 3.8 - - - +
401B ALA* 3.6 16.0 - - + +
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A ARG 4.3 2.3 - - - +
396A GLY* 3.3 24.9 - - - +
398A ALA* 5.3 1.1 - - - +
124B GLN* 5.1 3.5 + - - +
261B VAL* 3.6 31.4 + - - +
264B GLN* 3.3 38.0 - - - +
265B VAL* 3.8 15.3 - - - +
268B GLU* 4.2 10.5 + - - -
328B LEU 4.3 7.3 + - - -
329B CYS* 5.6 1.2 + - - +
390B TRP* 3.1 46.7 + - + +
391B CYS* 3.4 10.6 - - - +
392B PHE 3.2 0.2 - - - -
393B ALA* 1.3 76.8 - - - +
395B ARG* 1.3 63.6 + - - +
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Residues in contact with ARG 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A ARG 4.3 2.9 - - - +
395A ARG 5.1 1.6 - - - +
396A GLY* 4.4 1.1 - - - -
327B LEU 3.0 30.5 + - - +
328B LEU 3.9 11.9 - - - +
329B CYS 4.9 0.9 - - - -
330B GLY* 3.6 25.8 - - - +
331B GLY 5.0 1.4 - - - +
337B GLU* 2.9 40.8 + - - -
391B CYS 3.0 20.5 + - - +
392B PHE 3.0 8.0 + - - +
394B ARG* 1.3 81.3 - - - +
396B GLY* 1.3 57.6 + - - +
397B TRP* 3.3 39.9 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il